Changing the commenting style in the BQSR

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -32,13 +32,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -299,6 +297,4 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         return table;
     }
-
-
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -216,12 +216,14 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
      */
     public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         long countedSites = 0L;
-        if (tracker.getValues(RAC.knownSites).size() == 0) {                                                            // Only analyze sites not present in the provided known sites
+        // Only analyze sites not present in the provided known sites
+        if (tracker.getValues(RAC.knownSites).size() == 0) {
             for (final PileupElement p : context.getBasePileup()) {
                 final GATKSAMRecord read = p.getRead();
                 final int offset = p.getOffset();
 
-                if (readHasBeenSkipped(read) || isLowQualityBase(read, offset))                                         // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
+                // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
+                if (readHasBeenSkipped(read) || isLowQualityBase(read, offset))
                     continue;
 
                 if (readNotSeen(read)) {
@@ -234,10 +236,12 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
                     read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates));
                 }
 
-                if (!ReadUtils.isSOLiDRead(read) ||                                                                     // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
+                // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
+                if (!ReadUtils.isSOLiDRead(read) ||
                     RAC.SOLID_RECAL_MODE == RecalUtils.SOLID_RECAL_MODE.DO_NOTHING ||
                         RecalUtils.isColorSpaceConsistent(read, offset))
-                    recalibrationEngine.updateDataForPileupElement(p, ref.getBase());                                                             // This base finally passed all the checks for a good base, so add it to the big data hashmap
+                    // This base finally passed all the checks for a good base, so add it to the big data hashmap
+                    recalibrationEngine.updateDataForPileupElement(p, ref.getBase());
             }
             countedSites++;
         }

public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

@@ -103,7 +103,9 @@ public class BaseRecalibration {
             }
         }
 
-        RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);                                  // compute all covariates for the read
+        // Compute all covariates for the read
+        RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
+
         for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
             if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
                 read.setBaseQualities(null, errorModel);

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java

@@ -116,7 +116,8 @@ public class RecalUtils {
         if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES)
             optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user
 
-        if (argumentCollection.COVARIATES != null) {                                                                    // parse the -cov arguments that were provided, skipping over the ones already specified
+        // parse the -cov arguments that were provided, skipping over the ones already specified
+        if (argumentCollection.COVARIATES != null) {
             for (String requestedCovariateString : argumentCollection.COVARIATES) {
                 // help the transition from BQSR v1 to BQSR v2
                 if ( requestedCovariateString.equals("DinucCovariate") )
@@ -349,7 +350,6 @@ public class RecalUtils {
         return Utils.join(",", names);
     }
 
-
     public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
         outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
     }
@@ -542,7 +542,8 @@ public class RecalUtils {
         if (!ReadUtils.isSOLiDRead(read)) // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
             return true;
 
-        if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) {                                      // Haven't calculated the inconsistency array yet for this read
+        // Haven't calculated the inconsistency array yet for this read
+        if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) {
             final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG);
             if (attr != null) {
                 byte[] colorSpace;
@@ -774,6 +775,4 @@ public class RecalUtils {
                 return base;
         }
     }
-
-
 }

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java

@@ -198,7 +198,8 @@ public class RecalibrationReport {
         final long nErrors = (Long) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
         final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME);
 
-        final double estimatedQReported = hasEstimatedQReportedColumn ?                                                 // the estimatedQreported column only exists in the ReadGroup table
+        // the estimatedQreported column only exists in the ReadGroup table
+        final double estimatedQReported = hasEstimatedQReportedColumn ?
                 (Double) reportTable.get(row, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table
                 Byte.parseByte((String) reportTable.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table
 

public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java

@@ -87,7 +87,8 @@ public class ContextCovariate implements StandardCovariate {
 
         // store the original bases and then write Ns over low quality ones
         final byte[] originalBases = read.getReadBases().clone();
-        final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);   // Write N's over the low quality tail of the reads to avoid adding them into the context
+        // Write N's over the low quality tail of the reads to avoid adding them into the context
+        final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);
         
         final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();
         byte[] bases = clippedRead.getReadBases();